The concept of a “ hidden intermediate ” in a reaction pathway has been promoted by Dieter Cremer[cite]10.1021/ar900013p[/cite] and much invoked on this blog. When I used this term in a recent article of ours[cite]10.1021/jo401146k[/cite], a referee tried to object, saying it was not in common use in chemistry. The term clearly has an image problem.
We have been experimenting with full-colour 3D printing of molecular objects. I thought I might here share some of our observations. Firstly, I list the software used: Crystal structures as sources of ball&stick models ( e.g. the CCDC database). Gaussian style cube files for sources of wavefunctions.
The ultimate reduction in size for an engineer is to a single molecule. It’s been done for a car; now it has been reported for the pixel (picture-element).[cite]10.1021/ja404256s[/cite] The molecule above (X=O, NR, R=aryl, etc) has been shown to be capable of acting as a molecular pixel.
Valence shell electron pair repulsion theory is a simple way of rationalising the shapes of many compounds in which a main group element is surrounded by ligands. ClF 3 is a good illustration of this theory.
This potential example of a molecule on the edge of chaos was suggested to me by a student (thanks Stephen!), originating from an inorganic tutorial. It represents a class of Mo-complex ligated by two dithiocarbamate ligands and two aryl nitrene ligands (Ar-N:). I focus on two specific examples[cite]10.1039/A907382E[/cite], where R=R’ = H or Me, with crystal structures available for both.
I noted previously that some 8-ring cyclic compounds could exist in either a planar-aromatic or a non-planar-non-aromatic mode, the mode being determined by apparently quite small changes in a ring substituent. Hunting for other examples of such chemistry on the edge, I did a search of the Cambridge crystal database for metal sulfides.
The butterfly effect summarises how a small change to a system may result in very large and often unpredictable (chaotic) consequences. If the system is merely on the edge of chaos, the consequences are predictable, but nevertheless finely poised between e.g. two possible outcomes. Here I ask how a molecule might manifest such behaviour. Two examples of the molecule above are known, differing only in the nature of the R group.
A feature of a blog which is quite different from a journal article is how rapidly a topic might evolve. Thus I started a few days ago with the theme of dicarbon (C 2 ), identifying a metal carbide that showed C 2 as a ligand, but which also entrapped a single carbon in hexa-coordinated mode.
The title of this post summarises the contents of a new molecular database: www.molecularspace.org[cite]10.1021/jz200866s[/cite] and I picked up on it by following the post by Jan Jensen at www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called “ The Harvard Clean Energy Project: Large-scale computational screening and design of organic
